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WES Gene Package Disorders of Sex Development (DSD) Whole Exome Sequencing Gene package Disorders of Sex Development (DSD), version 5.1, 22‐11‐2017 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x AKR1C1 No OMIM phenotype 600449 66 100 100 94 AKR1C4 {46XY sex reversal 8, modifier of}, 614279 600451 52 100 100 93 AMH Persistent Mullerian duct syndrome, type I, 261550 600957 64 100 100 93 AMHR2 Persistent Mullerian duct syndrome, type II, 261550 600956 80 100 100 94 ANOS1 Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1), 308700 300836 44 100 93 75 AR Androgen insensitivity, 300068 313700 60 100 95 81 Androgen insensitivity, partial, with or without breast cancer, 312300 Hypospadias 1, 300633 {Prostate cancer, susceptibility to}, 176807 Spinal and bulbar muscular atrophy of Kennedy, 313200 ARX Epileptic encephalopathy, early infantile, 1, 308350 300382 42 89 80 65 Hydranencephaly with abnormal genitalia, 300215 Lissencephaly 2, 300215 Mental retardation 29 and others, 300419 Partington syndrome, 309510 Proud syndrome, 300004 ATRX Alpha‐thalassemia myelodysplasia syndrome, somatic, 300448 300032 40 100 91 76 Alpha‐thalassemia/mental retardation syndrome, 301040 Mental retardation‐hypotonic facies syndrome, 309580 BMP15 Ovarian dysgenesis 2, 300510 300247 52 100 100 86 Premature ovarian failure 4, 300510 CBX2 ?46XY sex reversal 5, 613080 602770 89 100 98 94 Whole exome sequencing Gene package Disorders of Sex Development (DSD) version 5.1, 22‐11‐2017 HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x CDKN1C Beckwith‐Wiedemann syndrome, 130650 600856 56 91 83 74 IMAGE syndrome, 614732 CHD7 CHARGE syndrome, 214800 608892 60 100 99 93 Hypogonadotropic hypogonadism 5 with or without anosmia, 612370 CREBBP Rubinstein‐Taybi syndrome 1, 180849 600140 81 100 99 91 CYB5A ?Methemoglobinemia, type IV, 250790 613218 47 100 100 89 CYP11A1 Adrenal insufficiency, congenital, with 46XY sex reversal, partial or complete, 613743 118485 68 100 100 100 CYP17A1 17‐alpha‐hydroxylase/17,20‐lyase deficiency, 202110 609300 80 100 100 98 17,20‐lyase deficiency, isolated, 202110 CYP19A1 Aromatase deficiency, 613546 107910 49 100 97 79 Aromatase excess syndrome, 139300 DHCR7 Smith‐Lemli‐Opitz syndrome, 270400 602858 84 100 100 100 DHH 46XY partial gonadal dysgenesis, with minifascicular neuropathy, 607080 605423 79 100 100 100 46XY sex reversal 7, 233420 DMRT1 No OMIM phenotype 602424 80 100 100 100 DMRT2 No OMIM phenotype 604935 71 100 99 92 FAM58A STAR syndrome, 300707 300708 50 81 81 80 FGF8 Hypogonadotropic hypogonadism 6 with or without anosmia, 612702 600483 94 99 94 94 FGFR1 Encephalocraniocutaneous lipomatosis, 613001 136350 70 100 100 96 Hartsfield syndrome, 615465 Hypogonadotropic hypogonadism 2 with or without anosmia, 147950 Jackson‐Weiss syndrome, 123150 Osteoglophonic dysplasia, 166250 Pfeiffer syndrome, 101600 Trigonocephaly 1, 190440 FGFR2 Antley‐Bixler syndrome without genital anomalies or disordered steroidogenesis, 207410 176943 49 100 98 81 Apert syndrome, 101200 Beare‐Stevenson cutis gyrata syndrome, 123790 Bent bone dysplasia syndrome, 614592 Craniofacial‐skeletal‐dermatologic dysplasia, 101600 Craniosynostosis, nonspecific Crouzon syndrome, 123500 Gastric cancer, somatic, 613659 Jackson‐Weiss syndrome, 123150 LADD syndrome, 149730 Pfeiffer syndrome, 101600 Saethre‐Chotzen syndrome, 101400 Scaphocephaly and Axenfeld‐Rieger anomaly Scaphocephaly, maxillary retrusion, and mental retardation, 609579 Whole exome sequencing Gene package Disorders of Sex Development (DSD) version 5.1, 22‐11‐2017 HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x FOXL2 Blepharophimosis, epicanthus inversus, and ptosis, type 1, 110100 605597 86 100 94 88 Blepharophimosis, epicanthus inversus, and ptosis, type 2, 110100 Premature ovarian failure 3, 608996 FSHB Hypogonadotropic hypogonadism 24 without anosmia, 229070 136530 58 100 100 100 FSHR Ovarian dysgenesis 1, 233300 136435 55 100 99 89 Ovarian hyperstimulation syndrome, 608115 Ovarian response to FSH stimulation, 276400 GATA4 Atrial septal defect 2, 607941 600576 42 100 86 65 Atrioventricular septal defect 4, 614430 ?Testicular anomalies with or without congenital heart disease, 615542 Tetralogy of Fallot, 187500 Ventricular septal defect 1, 614429 GNRHR Hypogonadotropic hypogonadism 7 without anosmia, 146110 138850 74 100 100 98 HOXA13 Guttmacher syndrome, 176305 142959 75 86 78 72 Hand‐foot‐uterus syndrome, 140000 HSD17B3 Pseudohermaphroditism, male, with gynecomastia, 264300 605573 42 100 95 79 HSD3B2 Adrenal hyperplasia, congenital, due to 3‐beta‐hydroxysteroid dehydrogenase 2 deficiency, 201810 613890 108 100 100 100 LHCGR Leydig cell adenoma, somatic, with precocious puberty, 176410 152790 55 100 98 84 Leydig cell hypoplasia with hypergonadotropic hypogonadism, 238320 Leydig cell hypoplasia with pseudohermaphroditism, 238320 Luteinizing hormone resistance, female, 238320 Precocious puberty, male, 176410 MAMLD1 Hypospadias 2, 300758 300120 65 100 97 93 MAP3K1 46XY sex reversal 6, 613762 600982 53 100 99 90 MCM8 ?Premature ovarian failure 10, 612885 608187 40 100 95 73 MCM9 Ovarian dysgenesis 4, 616185 610098 60 100 99 89 NR0B1 Adrenal hypoplasia, congenital, 300200 300473 77 100 100 99 46XY sex reversal 2, dosage‐sensitive, 300018 NR5A1 Adrenocortical insufficiency, 612964 184757 72 100 98 95 Premature ovarian failure 7, 612964 Spermatogenic failure 8, 613957 46, XX sex reversal 4, 617480 46XY sex reversal 3, 612965 NUP107 Nephrotic syndrome, type 11, 616730 607617 37 100 94 69 POR Antley‐Bixler syndrome with genital anomalies and disordered steroidogenesis, 201750 124015 84 100 100 100 Disordered steroidogenesis due to cytochrome P450 oxidoreductase, 613571 PROK2 Hypogonadotropic hypogonadism 4 with or without anosmia, 610628 607002 38 100 100 81 PROKR2 Hypogonadotropic hypogonadism 3 with or without anosmia, 244200 607123 138 100 100 100 PSMC3IP Ovarian dysgenesis 3, 614324 608665 73 100 100 100 Whole exome sequencing Gene package Disorders of Sex Development (DSD) version 5.1, 22‐11‐2017 HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x RSPO1 Palmoplantar hyperkeratosis and true hermaphroditism, 610644 609595 50 100 100 94 Palmoplantar hyperkeratosis with squamous cell carcinoma of skin and sex reversal, 610644 SOX3 Mental retardation, with isolated growth hormone deficiency, 300123 313430 56 100 96 89 Panhypopituitarism, 312000 SOX9 Acampomelic campomelic dysplasia, 114290 608160 66 100 100 99 Campomelic dysplasia, 114290 Campomelic dysplasia with autosomal sex reversal, 114290 SRD5A2 Pseudovaginal perineoscrotal hypospadias, 264600 607306 44 100 94 76 SRY 46XX sex reversal 1, 400045 480000 20 50 41 35 46XY sex reversal 1, 400044 STAG3 Premature ovarian failure 8, 615723 608489 65 100 98 93 STAR Lipoid adrenal hyperplasia, 201710 600617 75 100 100 100 SYCE1 ?Premature ovarian failure 12, 616947 611486 55 100 100 93 ?Spermatogenic failure 15, 616950 TSPYL1 Sudden infant death with dysgenesis of the testes syndrome, 608800 604714 87 100 100 100 WDR11 Hypogonadotropic hypogonadism 14 with or without anosmia, 614858 606417 59 100 98 86 WNT4 Mullerian aplasia and hyperandrogenism, 158330 603490 115 92 92 92 ?SERKAL syndrome, 611812 WT1 Denys‐Drash syndrome, 194080 607102 80 100 98 96 Frasier syndrome, 136680 Meacham syndrome, 608978 Mesothelioma, somatic, 156240 Nephrotic syndrome, type 4, 256370 Wilms tumor, type 1, 194070 ZFPM2 Diaphragmatic hernia 3, 610187 603693 60 100 100 100 Tetralogy of Fallot, 187500 46XY sex reversal 9, 616067 ‐ Gene symbols according HGCN ‐ OMIM release used: 2‐6‐2017 ‐ "No OMIM phenotypes" indicates a gene without a current OMIM association ‐ OMIM phenotypes between "[ ]", indicate "nondiseases," mainly genetic variations that lead to apparently abnormal laboratory test values ‐ OMIM phenotypes between "{}", indicate risk factors ‐ OMIM phenotypes with a question mark, "?", before the disease name indicates an unconfirmed or possibly spurious mapping ‐ The statistics above are based on a set of 96 samples ‐ Median depth is the median of the mean sequence depth over the protein coding exons (±10bp flanking introns) of the longest transcript ‐ % Covered 10x describes the percentage of a gene’s coding sequence (±10bp flanking introns) that is covered at least 10x ‐ % Covered 20x describes the percentage of a gene’s coding sequence (±10bp flanking introns) that is covered at least 20x Whole exome sequencing Gene package Disorders of Sex Development (DSD) version 5.1, 22‐11‐2017.
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